Align Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 257 bits (657), Expect = 2e-73 Identities = 141/302 (46%), Positives = 193/302 (63%), Gaps = 10/302 (3%) Query: 15 LILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAA 74 + LI + + L + + FLT+ N + V+ VS +S GMT+VI+T+GIDLSVGSIL Sbjct: 11 IALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSVGSILALC 70 Query: 75 SVVMGLLMDEK----------GLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLG 124 V L+ G +P +V++G+ +G G G NG IT+ ++ PF++TL Sbjct: 71 GAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPFVATLA 130 Query: 125 MLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTG 184 ML++ RGL + +GG+PI+ E F G G +P+PV AVI +A + K T G Sbjct: 131 MLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIPMPVWITAVIVALAVLLTKKTKFG 190 Query: 185 RRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELD 244 R +YAIGGN A++L GI R+ + VY I G LAA G ++T+ L AQPNAG YELD Sbjct: 191 RYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPNAGISYELD 250 Query: 245 VIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAI 304 IAA VIGGTSLSGG+GTI+GA LG +I+GVL NG++LL VS FWQQVV G VI++A+ I Sbjct: 251 AIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKGAVILLAVVI 310 Query: 305 DQ 306 D+ Sbjct: 311 DK 312 Lambda K H 0.328 0.145 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 330 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 313 Length of database: 318 Length adjustment: 27 Effective length of query: 286 Effective length of database: 291 Effective search space: 83226 Effective search space used: 83226 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory